physamp

sample sequence alignment corresponding to phylogeny

Command lineScience

Not tested on a device yet. What that means

Commands in the package

bppalnoptim
bppphysamp

About physamp

From Debian's package description

The PhySamp package currently contains two programs: bppphysamp, which samples sequences according to their similarity, and bppalnoptim, which samples a sequence alignment by removing sequences in order to maximize the number of sites suitable for a given analysis. The bppalnoptim program has three running modes:
Interactive: the user will be iteratively proposed a set of choices for sequence removal, with their corresponding site gains. The procedure stops when the user does not want to remove more sequences, and the resulting filtered alignment is written.
Automatic: the user enters an a priori criterion for stopping the filtering procedure (for instance a minimum number of sequences to keep).
Diagnostic: this mode allows one to plot the trade-off curve, by showing the site gain as a function of the number of removed sequences.

From Debian's description of the physamp package, under that package's license.

Dependencies

Depends on

libbpp-core4t64
libbpp-phyl12t64
libbpp-seq12t64
libc6
libgcc-s1
libstdc++6

Related apps

mafftMultiple alignment program for amino acid or nucleotide sequencesCommand line
kalignGlobal and progressive multiple sequence alignmentCommand line
probconsPROBabilistic CONSistency-based multiple sequence alignmentCommand line
prodamultiple alignment of protein sequencesCommand line
clustalwglobal multiple nucleotide or peptide sequence alignmentCommand line
hhsuitesensitive protein sequence searching based on HMM-HMM alignmentCommand line

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Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the physamp package, under that package's license.
Description: Debian's description of the physamp package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.